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- PDB-7zp7: Crystal structure of evolved photoenzyme EnT1.3 (truncated) with ... -

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Basic information

Entry
Database: PDB / ID: 7zp7
TitleCrystal structure of evolved photoenzyme EnT1.3 (truncated) with bound product
ComponentsEnT1.3 C
KeywordsBIOSYNTHETIC PROTEIN / Designed photoenzyme / [2+2]-cyclase / genetic code expansion / Engineered enzyme
Function / homologyChem-JRP
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHardy, F.J. / Levy, C.
Funding supportEuropean Union, United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)757991European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M027023/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/023755/1 United Kingdom
CitationJournal: Nature / Year: 2022
Title: A designed photoenzyme for enantioselective [2+2] cycloadditions.
Authors: Trimble, J.S. / Crawshaw, R. / Hardy, F.J. / Levy, C.W. / Brown, M.J.B. / Fuerst, D.E. / Heyes, D.J. / Obexer, R. / Green, A.P.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EnT1.3 C
B: EnT1.3 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9625
Polymers73,4692
Non-polymers4933
Water12,647702
1
A: EnT1.3 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9502
Polymers36,7351
Non-polymers2151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EnT1.3 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0123
Polymers36,7351
Non-polymers2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.752, 73.958, 74.722
Angle α, β, γ (deg.)90.000, 93.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein EnT1.3 C


Mass: 36734.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-JRP / (1~{R},10~{R},12~{S})-15-oxa-8-azatetracyclo[8.5.0.0^{1,12}.0^{2,7}]pentadeca-2(7),3,5-trien-9-one / (3aS,4aR,10bR)-3,3a,4,4a-tetrahydro-2H-furo[2',3':2,3]cyclobuta[1,2-c]quinolin-5(6H)-one


Mass: 215.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium formate dihydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→74.59 Å / Num. obs: 60455 / % possible obs: 99.64 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08916 / Net I/σ(I): 15.85
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 2.08 / Num. unique obs: 5861 / CC1/2: 0.876 / CC star: 0.966 / % possible all: 97.25

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3i1c

3i1c


Resolution: 1.7→74.59 Å / SU ML: 0.1378 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.5546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1807 3069 5.08 %
Rwork0.1507 57362 -
obs0.1523 60431 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 36 702 5549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00485064
X-RAY DIFFRACTIONf_angle_d0.87696887
X-RAY DIFFRACTIONf_chiral_restr0.0552718
X-RAY DIFFRACTIONf_plane_restr0.0074910
X-RAY DIFFRACTIONf_dihedral_angle_d8.9177691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.24041170.20152499X-RAY DIFFRACTION96.25
1.73-1.760.23361210.19422600X-RAY DIFFRACTION98.2
1.76-1.790.2141470.18272553X-RAY DIFFRACTION99.41
1.79-1.820.2121630.17692581X-RAY DIFFRACTION99.49
1.82-1.850.22051490.17582560X-RAY DIFFRACTION99.71
1.85-1.890.22321650.17512582X-RAY DIFFRACTION99.96
1.89-1.930.22751560.16872587X-RAY DIFFRACTION99.78
1.93-1.980.19791520.16482581X-RAY DIFFRACTION99.82
1.98-2.030.22881480.16242621X-RAY DIFFRACTION99.93
2.03-2.080.21251510.15392582X-RAY DIFFRACTION99.89
2.08-2.140.19391210.15382640X-RAY DIFFRACTION100
2.14-2.210.16951610.1522581X-RAY DIFFRACTION99.93
2.21-2.290.18841170.15372644X-RAY DIFFRACTION100
2.29-2.380.18571060.14432640X-RAY DIFFRACTION100
2.38-2.490.18961210.15162649X-RAY DIFFRACTION100
2.49-2.620.17541100.14962620X-RAY DIFFRACTION100
2.62-2.790.17131150.15292657X-RAY DIFFRACTION100
2.79-30.18421720.1522613X-RAY DIFFRACTION100
3-3.30.17461400.14342606X-RAY DIFFRACTION100
3.3-3.780.16011560.1392614X-RAY DIFFRACTION100
3.78-4.760.12411410.11652657X-RAY DIFFRACTION99.96
4.76-74.590.18441400.15922695X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 11.9587096889 Å / Origin y: -22.8628780688 Å / Origin z: 17.3503886835 Å
111213212223313233
T0.131370151068 Å2-0.00957599864042 Å2-0.0172679127616 Å2-0.130407800107 Å20.000783960327311 Å2--0.13941505592 Å2
L0.340856849994 °2-0.278060938593 °2-0.0181377047324 °2-0.601955188805 °20.0275204335935 °2--0.122990828403 °2
S-0.00843221511808 Å °0.00395485989456 Å °-0.00440267064513 Å °0.00914125674881 Å °0.00216574740863 Å °-0.000571426609476 Å °0.000960733195995 Å °-0.00373302549454 Å °0.00622012898285 Å °
Refinement TLS groupSelection details: all

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